SpliceCraft is a plasmid workbench that runs where you already work. Open a map, edit the sequence, design primers, plan a Golden Braid or MoClo assembly, BLAST a hit, check your Sanger reads, and keep a lab notebook — all from the keyboard, in one place, no browser tab and no cloud account. Circular and linear maps render as crisp Unicode braille graphics in any modern terminal, and export to publication-quality PNG or SVG.
It's built by a practicing bioengineer for daily bench work: the bug reports come from real cloning, and so do the fixes.
Why give it a try:
- Fast and local. No Electron, no web app, no login.
pipx install splicecraftand you're designing in seconds. - It does the whole job. View → edit → design → clone → simulate → verify → document — one tool that understands how those steps connect.
- It guards your data like it's irreplaceable (because it is — see below).
- It's scriptable. A 230+ endpoint local API and a stdlib CLI let an agent or a shell script drive every workflow.
pipx install splicecraft
splicecraft # empty canvas
splicecraft L09137 # fetch pUC19 from NCBI on launch
splicecraft myplasmid.gb # local GenBank or .dnaPress ? once running for the keyboard reference, or Ctrl+K for a fuzzy
command palette that jumps straight to any tool by name.
x86-64 Linux, Intel macOS, and Windows install entirely from prebuilt wheels.
On ARM64 Linux and Apple Silicon, one dependency (primer3-py) has no
ARM wheel and compiles at install, so install a C toolchain first
(sudo apt install build-essential python3-dev, or xcode-select --install).
On Windows, use Windows Terminal — the console is auto-configured for
UTF-8 + ANSI at startup, though this path is CI-tested via mocks and not yet
confirmed on real Windows hardware. If braille shows as boxes, toggle
'ASCII plasmid map' in Settings → Display.
Full matrix: docs/PLATFORMS.md · other install methods:
docs/install.md.
Your plasmid library is months — sometimes years — of work, so SpliceCraft is built to be a daily driver you never have to worry about:
- Your data is sacred. Every save is atomic, backed up (
.bak+ rotating timestamps + daily snapshots), and guarded by a "suspicious shrink" refusal that won't replace a 156 MB library with an empty file. Name collisions always ask — skip / copy / overwrite — and self-updates snapshot everything first. Bulk actions preview what they'll do, and one press ofuputs the whole batch back. - The biology is correct, and proven. Palindromes, Type IIS, origin-spanning cuts, wrap-around features, non-standard genetic codes, and IUPAC are pinned to the base — behind 4,000+ tests plus property-based fuzzing on the biology, crash-injection on the save path, and concurrency fuzzing on the data layer.
- We go looking for trouble. A long list of sacred invariants
(
CLAUDE.md) and multi-pass pre-release audits hunt edge cases, data-loss windows, races, and security gaps before they reach you.
Details: docs/data-safety.md ·
SECURITY.md.
Everything hangs off a menu bar across the top, read left to right. Full
reference: docs/features.md.
Search without leaving the app (Ctrl+B). Local runs BLASTN / BLASTP /
HMMscan against your own library in-process via pyhmmer — no external
blast+ to install — with a one-click Pfam-A / NCBIfam downloader. Online
sends DNA, protein, a feature, or a whole plasmid to NCBI or EMBL-EBI and
tables the hits, with a Cancel that really stops. Agents can only search online
once you tick the setting for it, so a script can never silently ship your
sequences off-box.
Drive the restriction overlay — all sites, unique cutters, 6+/4+ bp, or just the Golden Braid connectors. Multi-cutters wear a live superscript cut-count (EcoRI², BsaI³) that ticks down as you edit a site out. Build named enzyme collections from the 200+ NEB catalog plus your own customs; the active collection scopes every scan.
A library for your reusable annotations — promoters, RBSs, tags, CDSs. Capture a region off any plasmid, then drop it onto another to annotate or splice it in. Ctrl+F finds a subsequence fuzzily on both strands; Ctrl+C on a CDS copies the protein rather than the DNA. Alt+Shift+R flips the whole record end-for-end with every feature re-framed; Alt+Shift+O re-cuts a circular plasmid so the cursor becomes base 1 — a real, undoable edit, refused on a linear record. File ▸ Find ORFs runs a wrap-aware six-frame scan.
A full-screen Primer3 designer for detection, cloning, Golden Braid, and generic primers, each with a Designed → Ordered → Validated lifecycle. The Primer Check tab runs in-silico PCR across your library: one primer lists every plasmid it anneals to with % identity, strand, and position; two add the amplicon length and the feature amplified, ranked ✓ / ⚠ / ~ / ✗. Binding is judged on the 3′ end, so a 5′ cloning tail lowers identity rather than vanishing. The library organises into collections with fuzzy search, and exports order-ready CSV — generic or the IDT bulk-upload template.
Site-directed mutagenesis. Point at a CDS, name the change (L54A), and
SpliceCraft designs the SOE-PCR primers — falling back to a 2-primer
modified-outer strategy near the ends, and only offering the shortcut when the
primer genuinely carries the change, so you never amplify wild-type by
accident. It also turns a pasted protein into an orderable CDS with
frequency-matched codon optimization.
Its Scrub tab cures a whole plasmid of restriction sites with no cloning: pick the enzymes and SpliceCraft finds the minimal point changes that kill each site — silent across every overlapping reading frame, never spawning a new one, and reported when a site can't be cured silently. Apply cure re-circularizes by QuikChange or Golden Braid, really digesting and ligating each amplicon, so History reads as a genuine assembly.
A gene-synthesis composer in three tabs. DNA is a scrolling linear editor with strand markers, feature stripes, live translation, feature-aware paste, click-to-highlight restriction sites, and zoom-to-overview. Protein fills codons in from your chosen table as you type, with a built-in motif library (His6, FLAG, HA, TEV, P2A, NLS, +30) and a tabbed codon-table manager that builds tables from an NCBI genome, a local CDS file, Kazusa, or TSV. Operon Design reverse-designs every RBS in its real assembled context, and domesticates a natural operon by curing forbidden Type IIS sites with primer-encoded synonymous edits.
Compose a part, hit Clone Fragment, and pick a path: a modular grammar hands it to the Domesticator; Gibson or Traditional open the Constructor. Ordering synthetic instead? L0 Fragment wraps the sequence in the correct nested overhangs for direct synthesis — two-tier aware, so a category pair nests inside the entry vector's external pair automatically.
Your Parts Bin — the Level-0 blocks for grammar-based assembly, in per-grammar bins. Multiple bins live side by side as collections, so a yeast toolkit and a plant toolkit never get mixed up.
The assembly bench: Traditional, Gibson, Golden Braid, MoClo, or your own
grammar, driven by a 4-source part picker. Every assembly lands as one library
entry carrying every parent feature forward, so you can trace a finished L3
construct back to its L0 parts. Deleted something by mistake? u brings it
back — the last 100 deletions of the session are undoable.
Ordered a synthetic fragment and it arrived? New Part from Syn Frag runs the cloning — cutting fragment and entry vector, ligating, closing the circle — then files the part and saves the finished L0 plasmid with its History. A fragment whose ends don't match the type you picked is turned away rather than filed as a part that can't assemble.
In-silico PCR and agarose gels. Pick a template, run the PCR, then save the
amplicon or send it to a gel lane. Gels render at 0.5–4% on a real
Helling–Goodman–Boyer mobility curve; stack lanes, save a gel to reload later,
or cite it as &<gel> in your notebook.
Verify constructs against real reads. Drop in a Plasmidsaurus .zip or fetch a
run straight from their API, then walk run → sample → target and Align: the
read lands as a colored bar (blue match / red mismatch / gray gap) on the
linear map — click it to jump the sequence panel to that exact spot. Bulk
auto-align matches a whole folder in one pass. The Verification Report
grades every construct (✓ verified / ⚠ near / ~ partial / ✗ divergent), and a
true sub-100% identity never rounds up to "100%".
A genuine lab notebook in markdown: a split-pane editor, entries grouped into
projects, and live colored cross-references — type @plasmid, !action,
or &gel and Ctrl+G jumps to the source. Attach images, previewed inline,
and spellcheck with F7.
Every plasmid remembers how it was made. History opens with a Protocol — a numbered recipe that reads left → right like the bench — above a lineage tree you can drill into as deep as you like. Pick any step and you get everything the record holds: what it did and where, the conditions, the primers with each binding site's position, strand and Tm, the fragment's end chemistry, and the enzymes regenerated.
If a record claims something the plasmid doesn't bear out — a site that isn't
there, a primer that no longer binds — the view says so instead of presenting
it as fact. It only ever reports: your sequences and your history are never
edited to make a warning disappear. Lineage rides along through .dna import /
export, and recover-history-from-dna finds the original by sequence — even
under a different name — to put a lost build record back.
A chat assistant that lives next to your plasmids: a direct conversation with a local Ollama model — no cloud, no API key, nothing leaves your machine. Streaming markdown answers, a ❤ context lifebar, slash commands, and a copy-pasteable transcript (Ctrl+E exports it).
Flip Agent on and Babs can drive SpliceCraft herself, calling the same
endpoints the --agent API exposes — read the plasmid, design primers, run a
digest, clone, manage the library, even drive the OT-2 — with everything
showing up live in the app. She asks before every write by default;
destructive whole-library wipes are never reachable, and physical robot
motion always asks first. Turn Corpus on and answers come grounded in a
research corpus with cited sources, grown by the built-in paper scraper and
topic-focused Learn crawls, or by indexing your own library into a pack
that is private by construction. Online database lookups (FPbase, UniProt,
Europe PMC, NCBI, patents) stay off until you tick the setting, and even then
only your query string is sent — never your sequence.
Needs Ollama running locally; splicecraft babs-setup bootstraps the engine in
one command. Details: docs/features.md.
SpliceCraft drives an Opentrons OT-2 liquid handler. Find Robots scans your network for OT-2s; the Deck draws the robot top-down as a clickable grid you fill with labware; the Designer builds an ordered step sequence (transfer, distribute, consolidate, mix, delay, pause). A Library tab binds a deck plate to a plasmid collection so wells map to your plasmids — then cherry-pick, replate by identity, or normalise DNA to a target ng/µL. Compile to a real Opentrons protocol, analyze on the robot's simulate, and run it behind Arm + a clean analysis + health, calibration, pipette and door checks, with live Pause / Resume / Abort and a telemetry panel (state, progress + ETA, fault banner). Every bit of it is scriptable.
File opens / fetches (NCBI) / saves / exports (GenBank · FASTA · GFF3 ·
map image as PNG/SVG, one plasmid or a whole collection), bulk-imports a
folder, and restores from backup; every GenBank it writes stamps a traceable
Created by SpliceCraft v… COMMENT. It also hosts the selection → cloning
hub (Alt+Shift+P): highlight any DNA and pick Traditional, Golden Braid /
MoClo, or Gibson — each opens pre-loaded with the selection and its features.
Migrate Data packages your entire setup into one checksum-verified .zip
to move between machines; Master Delete is a triple-gated full wipe.
Settings collects every toggle plus the grammar, entry-vector,
enzyme-collection, and codon-table editors.
A 230+ endpoint localhost JSON API (splicecraft --agent, or --headless for
a no-UI server with a /healthz probe) and a stdlib-only CLI
(splicecraft-cli, including a call passthrough to every endpoint) drive
every workflow. /tools self-describes each endpoint's request schema. See
docs/agent-api.md and docs/cli.md.
| Topic | Where |
|---|---|
| Install methods | docs/install.md |
| First five seconds with pUC19 | docs/getting-started.md |
| Full feature list | docs/features.md |
| Keybindings + menus | docs/keybindings.md |
| Data safety + backups | docs/data-safety.md |
| Agent API (HTTP) | docs/agent-api.md |
| CLI sidecar | docs/cli.md |
| Architecture | docs/architecture.md |
| Sacred invariants | CLAUDE.md |
| Contributing | CONTRIBUTING.md |
| Security policy | SECURITY.md |
| Changelog | CHANGELOG.md |
python3 -m pytest -n auto -q # full suite (~5–6 min on 8 cores)
python3 -m pytest tests/test_dna_sanity.py # biology correctness only (< 2 s)All tests run offline against synthetic SeqRecords and monkeypatched data
paths; the autouse _protect_user_data fixture guarantees no test can write to
real user files.
Actively maintained by a practicing bioengineer running real cloning workflows
in it daily; releases typically go out the same week a problem surfaces at the
bench. Issues and PRs welcome — see CONTRIBUTING.md before
opening a non-trivial one.
If SpliceCraft did part of the work in something you publish, please cite it.
Every release is archived on Zenodo with its own DOI, so
a methods section can point at the exact version that produced the design. The
concept DOI 10.5281/zenodo.21960400
always resolves to the newest release.
splicecraft --citation # APA reference + BibTeX, pinned to your versionThe repository also ships a CITATION.cff, so GitHub's Cite
this repository button exports APA or BibTeX directly.
MIT